table = read.table(file = 'Orthogroups.GeneCount_TIdeS_12-2.tsv', sep = '\t', header = TRUE)
taxon = read.table(file = 'taxon.csv', sep = ',', header = TRUE)
arcellinidaonly <- by_group %>%
filter(Group_1 > 1 & Group_2 > 2 & Group_3 > 2 & Group_4 > 1 & Group_6 > 0 & Group_8 > 3 & Group_7/(Group_1+Group_2+Group_3+Group_4+Group_5+Group_6+Group_8+Group_7) < 0.05)
#saving to table
arcellinida_OGs <- merge(reduced_table_with_row_name, arcellinidaonly,
by = 'row.names', all = FALSE)[1:225]
names(arcellinida_OGs)[names(arcellinida_OGs) == 'Row.names'] <- 'Orthogroup'
write.table(arcellinida_OGs, sep="\t", file="Tables/LSGarcellinida.tsv", row.names = FALSE)
#calculate number of LSG
number <- nrow(arcellinidaonly)
Criteria: at least 2 from Sphaerothecina, 3 H. elegans, 3 Nebela, 2 Difflugina, 1 Heleopera, 1 from misc Arcellinida groups, and less than 5% non Arcellinida
There are 122 all-Arcellinida lineage-specific genes.
hpapilio_only <- by_group %>%
filter(Group_8 > 20 & ((Group_8/(Group_1+Group_2+Group_3+Group_4+Group_5+Group_6+Group_7+Group_8)) > 0.95))
#saving to table
hpapilio_OGs <- merge(reduced_table_with_row_name, hpapilio_only,
by = 'row.names', all = FALSE)[1:225]
#rename column name
names(hpapilio_OGs)[names(hpapilio_OGs) == 'Row.names'] <- 'Orthogroup'
write.table(hpapilio_OGs, sep="\t", file="Tables/LSGpapilio.tsv", row.names = FALSE)
#calculate number of LSG
number_pap <- nrow(hpapilio_only)
Criteria: at least 20 H. papilio cells, 5% of other cells can be non-H. papilio
There are 129 H. papilio-only lineage-specific genes.
helegans_only <- by_group %>%
filter(Group_2 > 7 & ((Group_2/(Group_1+Group_2+Group_3+Group_4+Group_5+Group_6+Group_7+Group_8)) > 0.95))
#saving to table
elegans_OGs <- merge(reduced_table_with_row_name, helegans_only,
by = 'row.names', all = FALSE)[1:225]
#rename column name
names(elegans_OGs)[names(elegans_OGs) == 'Row.names'] <- 'Orthogroup'
write.table(elegans_OGs, sep="\t", file="Tables/LSGelegans.tsv", row.names = FALSE)
#calculate number of LSG
number_elegans <- nrow(helegans_only)
Criteria: at least 7 H. elegans cells, 5% of other cells can be non-H. elegans
There are 92 H. elegans-only lineage-specific genes.
newtable_heat <- newtable[,-1]
rownames(newtable_heat) <- newtable[,1]
#saving to binary table
arcellinida_heat <- merge(newtable_heat, arcellinidaonly,
by = 'row.names', all = FALSE)[1:224]
#rename column name
names(arcellinida_heat)[names(arcellinida_heat) == 'Row.names'] <- 'Orthogroup'
arcellinida_heat_x <- arcellinida_heat[,-1]
rownames(arcellinida_heat_x) <- arcellinida_heat[,1]
data <- as.matrix(arcellinida_heat_x)
fig <- plot_ly(z = data, y=rownames(arcellinida_heat_x), x=colnames(arcellinida_heat_x), colors = colorRamp(c("white", "red")), type = "heatmap") %>%
layout( plot_bgcolor='#e5ecf6',
yaxis = list(
showticklabels = FALSE,
gridcolor = 'ffff'))#generate an interactive heat map
fig #view
newtable_heat <- newtable[,-1]
rownames(newtable_heat) <- newtable[,1]
#saving to binary table
papilio_heat <- merge(newtable_heat, hpapilio_only,
by = 'row.names', all = FALSE)[1:225]
#rename column name
names(papilio_heat)[names(papilio_heat) == 'Row.names'] <- 'Orthogroup'
papilio_heat_x <- papilio_heat[,-1]
rownames(papilio_heat_x) <- papilio_heat[,1]
data <- as.matrix(papilio_heat_x)
fig <- plot_ly(z = data, y=rownames(papilio_heat_x), x=colnames(papilio_heat_x), colors = colorRamp(c("white", "red")), type = "heatmap") %>%
layout( plot_bgcolor='#e5ecf6',
yaxis = list(
showticklabels = FALSE,
gridcolor = 'ffff'))#generate an interactive heat map
fig #view
newtable_heat <- newtable[,-1]
rownames(newtable_heat) <- newtable[,1]
#saving to binary table
elegans_heat <- merge(newtable_heat, helegans_only,
by = 'row.names', all = FALSE)[1:225]
#rename column name
names(elegans_heat)[names(elegans_heat) == 'Row.names'] <- 'Orthogroup'
elegans_heat_x <- elegans_heat[,-1]
rownames(elegans_heat_x) <- elegans_heat[,1]
data <- as.matrix(elegans_heat_x)
fig <- plot_ly(z = data, y=rownames(elegans_heat_x), x=colnames(elegans_heat_x), colors = colorRamp(c("white", "red")), type = "heatmap") %>%
layout( plot_bgcolor='#e5ecf6',
yaxis = list(
showticklabels = FALSE,
gridcolor = 'ffff'))#generate an interactive heat map
fig #view